Rcircos: Need Guidance

Question

[ChIP]

Hi!

I am trying to use RCircos (R version of Circos) to plot Ideogram from my data (set of peaks) which is in genome hg18

sample set of peaks

chr1    9125755    9126385
chr1    9222015    9222867
chr1    9408512    9409751
chr1    9612112    9612961
chr1    9687229    9687962
chr1    9875516    9876245

what I have done in R

library(RCircos)
data<-read.table("peakset")
names(data) = c("Chromosome", "chromStart", "chromEnd")

now data looks like this:

Chromosome chromStart chromEnd
chr1    9125755    9126385
chr1    9222015    9222867
chr1    9408512    9409751
chr1    9612112    9612961
chr1    9687229    9687962
chr1    9875516    9876245

ofcourse there are peaks in other chromosomes as well.

after this I am kind of lost.

Please help, if you have used this tool to plot your data on Ideogram, I know it is bit naive question but please share your knowledge if you have used this tool for the purpose of drawing Ideogram.

Thank you in anticipation.

[Vassia]

Hi, ChIP I am having the same trouble with Rcircos I have tried running the code suggested by R-packages website for the demo human ideogram but I am still getting errors. The main error I am getting is "Some chromosomes in plot data are not in ideogram" and I have tried changing the parameters and use hg38 as cyto.info but still nothing. And my pdf does not open at all saying that is damaged. I was wondering if you have managed to solve your question and you can share your knowledge for this package.

Thank you in advance

Answer 1

[Zev.Kronenberg]

Have you tried any of the examples in the documentation? They provide good documentation.

http://cran.r-project.org/web/packages/RCircos/RCircos.pdf

# Load RCircos libaray
# __________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
library(RCircos);
# Load human chromosome ideogram
# __________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
data(UCSC.HG19.Human.CytoBandIdeogram);
# Set RCircso core components
# __________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
chr.exclude <- NULL;
num.inside <- 5;
num.outside <- 0;
## Not run: RCircos.Set.Core.Componentscyto.info,
chr.exclude, num.inside, num.outside);
## End(Not run)
# Initialize graphic device and plot chromosome
# ideogram
# __________________________________________________
# xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
## Not run: RCircos.Set.Plot.Area();
## Not run: RCircos.Chromosome.Ideogram.Plot();

[ChIP]

Hi! I did try but failed. secodly I need hg18 and not 19. :(... Could you please guide me with my data set how can i plot it.

[Josh Herr]

Hello ChIP. This is very difficult request based on what you have provided us and the confines of helping you from a long distance away does not make this easy for anyone to help you. Perhaps it would be best for you to have some one-on-one time with someone who is comfortable with R and will help you through the process. With your request for "Please help me do this..." it's not evident that you have have put any effort into answering your question yet.

[Zev.Kronenberg]

how did it fail? remove the comments from '##' Not run: RCircos.Set.Plot.Area(); '##'Not run: RCircos.Chromosome.Ideogram.Plot(); and run them.

Answer 2

[Andrewoods]

Maybe you want to try shinyCircos. It's an interactive APP. https://github.com/venyao/shinyCircos http://shinycircos.ncpgr.cn/

[Ram]

Please stop spamming posts with the same comment. Create a Tool post to showcase your application.